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Ancient DNA sheds light on Native American origins

Geneticists have identified the genome of the oldest human remains on the American continent from a child buried 12,600 years ago. Erin Brodwin reports.

A distinctive two-faced stone blade similar to the one buried with the Clovis boy. – Sarah L. Anzick

Piecing together DNA fragments from a child buried 12,600 years ago in North America, scientists found themselves looking for the first time at the genome of the oldest human remains on the American continent. Belonging to an infant boy of the Clovis people, the genome is extremely similar to that of present-day Native Americans. It’s a finding that establishes the Clovis as the ancestors of Native Americans and that the Clovis themselves were descended from East Asian people. The findings overturn controversial views that the Clovis were descendants of Western Europeans and not the ancestors to Native Americans.

“The Clovis child is a direct ancestor of all the indigenous peoples living in North and South America. It’s pretty remarkable; [the genome provides] a missing link,” says University of Copenhagen geneticist Eske Willerslev, who led the analysis of the ancient DNA. “The child was unequivocally Asian,” adds co-author archaeologist Michael Walters, from University of Texas A&M.

The 12,600-year-old skeleton, exhumed from an ochre-dusted burial site discovered in Montana in 1968, belongs to an infant boy. The tools he was buried with include highly distinctive bi-faced stone blades, and identify him as a representative of the Clovis culture – named for the site near Clovis, New Mexico where such tools and human remains were first found in the 1930s. Similar remains have since been found across North America, and represent the first humans to arrive on the American continent.

It's likely the Clovis child’s ancestors started out in Asia and divided into two populations as they moved toward the Americas.

Yet, for more than 80 years, scientists disagreed on where the Clovis people’s ancestors came from. Some theorised they trekked out of East Asia, crossing the narrow land bridge that is now the Bering strait. But the Solutrean hypothesis proposed that they descended from southwestern Europeans who crossed the Atlantic in small boats when much of it was covered in pack ice during the last glacial maximum 19,000 years ago.

The new analysis of the Clovis child's DNA, published in Nature in February, rules out the second hypothesis, says Waters. Willerslev goes even further. Building on an earlier study of ancient DNA from an older skeleton in Siberia, he says it's likely the Clovis child’s ancestors started out in Asia and divided into two populations as they moved toward the Americas. While the first group settled in what we now call Canada, the child’s ancestors kept going south, populating North and South America.

These new insights only came to light thanks to technical advances that make it possible to take shredded bits of ancient DNA, read their sequence and piece them together – so-called “Next Generation” sequencing. The team extracted the DNA from fragments of the Clovis boy’s skull and painstakingly pieced together his entire genome.

The burial site of the Clovis boy. The pole, centre left, marks the grave. – Mike Waters

Willerslev’s decision to look at the boys’ entire genome contrasts with previous genetic research on ancient skeletons, where scientists studied bits of the genome. "You have a lot of people pull out parts of the genome they want to study and just sequence those,” says University of Copenhagen researcher Maanasa Raghavan, who was not involved in the study. Scientists then take those chunks and fill in the gaps with data from previously sequenced genomes. But since the vast majority of sequenced DNA is from Europeans, the final appearance of the genome could be skewed toward resembling that of a European, Raghavan says.

By sequencing the Clovis child's entire genome, Willerslev could avoid that bias. He then paid particular attention to five distinctive clusters of DNA, called “haplogroups”, which provide insight into where a group of people may have emerged. In the child, “four of them clearly linked to Asia,” says Willerslev. But the fifth, “Haplogroup X”, links to Europe.

How did Haplogroup X get in there? The answer, he says, is that Clovis ancestors were likely to have been the progeny of two groups: one comprised of east Asians travelling north, and a group that had long ago trekked east out of Europe to settle in Siberia. They met, Willerslev suspects, in a northern region that includes part of Russia and Alaska called Beringia, where they interbred to give rise to the Clovis people.

“The generic belief is that Native Americans derived from one ancestral population, but Willerslev showed it was much more complex,” says Raghavan. The finding explains how ancient Native Americans could have the European Haplogroup X in their DNA, despite arriving on the content from East Asia.

Contemporary Native Americans still carry Haplogroup X. It’s further genetic evidence they are direct descendants of the Clovis and their ancestors, the first people to successfully settle the Americas.